In this notebook, we are using the maf_autopsy.tsv file
generated from the 01-preprocess-data.Rmd script. We will
also use the oncoprint goi list from OpenPedCan
oncoprint-goi-lists-OpenPedCan-gencode-v39.csv.
suppressPackageStartupMessages({
library(tidyverse)
library(ggrepel)
library(reshape2)
})
# Detect the ".git" folder. This will be in the project root directory.
# Use this as the root directory to ensure proper sourcing of functions
# no matter where this is called from.
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
scratch_dir <- file.path(root_dir, "scratch")
analysis_dir <- file.path(root_dir, "analyses", "tmb-vaf-longitudinal")
input_dir <- file.path(analysis_dir, "input")
# Input files
maf_autopsy_file <- file.path(scratch_dir, "maf_autopsy.tsv")
oncoprint_goi_file <- file.path(input_dir, "oncoprint-goi-lists-OpenPedCan-gencode-v39.csv")
palette_file <- file.path(root_dir, "figures", "palettes", "timepoint_color_palette.tsv")
# File path to plots directory
plots_dir <-
file.path(analysis_dir, "plots")
if (!dir.exists(plots_dir)) {
dir.create(plots_dir)
}
# File path to results directory
results_dir <-
file.path(analysis_dir, "results")
if (!dir.exists(results_dir)) {
dir.create(results_dir)
}
source(paste0(analysis_dir, "/util/function-create-corplot.R"))
source(paste0(root_dir, "/figures/scripts/theme.R"))
# Read maf_autopsy file generated from step `01-process-data.Rmd`
maf_autopsy_raw <- readr::read_tsv(maf_autopsy_file, guess_max = 100000, show_col_types = FALSE) %>%
group_by(Kids_First_Participant_ID) %>%
mutate(cg_distinct = n_distinct(cancer_group) > 1) # to identify samples with different diagnosis across timepoints
# So far we have one PT_1H2REHT2 patient case with a secondary diagnosis in one of the progressive samples
# To reflect situations with multiple diagnosis, we will create `cg_sum column`
maf_autopsy <- maf_autopsy_raw %>%
distinct(cancer_group, .keep_all = TRUE) %>%
summarise(cg_sum = str_c(cancer_group, collapse = ",")) %>%
left_join(maf_autopsy_raw, by = c("Kids_First_Participant_ID"))
# Read oncoprint_goi_file
# We will use the following list of genes and then we will create a label to select the ones for the corplots.
oncoprint_goi <- read.csv(oncoprint_goi_file, stringsAsFactor = FALSE) %>%
select(LGAT, Embryonal.tumor, HGAT, Other)
# let's create a list with the genes to be used for the corplots
oncoprint_goi <- data.frame(goi_list = unlist(oncoprint_goi))
# remove empty rows
oncoprint_goi <- oncoprint_goi[!apply(oncoprint_goi == "", 1, all), ]
oncoprint_goi <- data.frame(oncoprint_goi)
# Read palette_df file
palette_df <- readr::read_tsv(palette_file, guess_max = 100000, show_col_types = FALSE)
# Save results by cg_sum
cg_names <- unique(as.character(maf_autopsy$cg_sum))
cg_names <- sort(cg_names, decreasing = FALSE)
print(cg_names)
[1] "Adamantinomatous Craniopharyngioma" "Atypical Teratoid Rhabdoid Tumor"
[3] "Chordoma" "Diffuse midline glioma"
[5] "Ependymoma" "Ewing sarcoma"
[7] "High-grade glioma" "High-grade glioma,Low-grade glioma"
[9] "Medulloblastoma"
# Create empty list for df
df_list <- list()
# Loop through cg_sum
for (x in seq_along(cg_names)){
print(x)
cg_maf_sub <- maf_autopsy %>%
filter(cg_sum == cg_names[x])
# We will define samples based on the "Kids_First_Participant_ID" column
samples <- unique(as.character(cg_maf_sub$Kids_First_Participant_ID))
print(samples)
# Define cg_sum specific plots dir
cg_plots_dir <- file.path(plots_dir, cg_names[x])
if (!dir.exists(cg_plots_dir)) {
dir.create(cg_plots_dir)
}
# Run loop for each sample and pair
for (i in seq_along(samples)) {
print(i)
maf_sub <- cg_maf_sub %>%
filter(Kids_First_Participant_ID == samples[i])
timepoints_other_plots <- unique(maf_sub$timepoints_other)
timepoints_other_plots <- timepoints_other_plots[!timepoints_other_plots == "4"]
print(timepoints_other_plots)
timepoints_deceased_plots <- unique(maf_sub$timepoints_deceased)
timepoints_deceased_plots <- timepoints_deceased_plots[!timepoints_deceased_plots %in% c("1", "2", "3")]
print(timepoints_deceased_plots)
# Run corplot function
for (t in seq_along(timepoints_deceased_plots)){
for (k in seq_along(timepoints_other_plots)){
# Plot the corplots
fname <- paste0(cg_plots_dir, "/", samples[i], "-", timepoints_other_plots[k], "-vs-", timepoints_deceased_plots[t], "-vaf-corplot.pdf")
print(fname)
p <- create_corplot(maf = maf_sub,
timepoints_other_plot = timepoints_other_plots[k],
timepoints_deceased_plot = timepoints_deceased_plots[t],
sid = samples[i])
pdf(file = fname, width = 10, height = 8)
print(p)
dev.off()
# Print df per pair
m <- create_corplot_melt(maf = maf_sub,
timepoints_other_plot = timepoints_other_plots[k],
timepoints_deceased_plot = timepoints_deceased_plots[t],
sid = samples[i])
# Assign name to df and store all df in list
df_name <- paste(samples[i], timepoints_other_plots[k], timepoints_deceased_plots[t], sep = "-")
df <- assign(df_name, m)
df_list[[df_name]] <- df
}
}
}
}
[1] 1
[1] "PT_WYXTEG3E"
[1] 1
[1] "Progressive_BS_G9B420R9"
[1] "Deceased_BS_H13TBC1X"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Adamantinomatous Craniopharyngioma/PT_WYXTEG3E-Progressive_BS_G9B420R9-vs-Deceased_BS_H13TBC1X-vaf-corplot.pdf"
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation ideoms with `aes()`
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 2
[1] "PT_3KM9W8S8" "PT_6N825561" "PT_DVXE38EX" "PT_RJ1TJ2KH"
[1] 1
[1] "Diagnosis_BS_859AV1DB"
[1] "Deceased_BS_2NQXY528" "Deceased_BS_4BB136DY" "Deceased_BS_EQQZ90JQ"
[4] "Deceased_BS_MS8TBCWJ" "Deceased_BS_P8FXRTZ2" "Deceased_BS_QR84QJN4"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_2NQXY528-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_4BB136DY-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_EQQZ90JQ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_MS8TBCWJ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_P8FXRTZ2-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_QR84QJN4-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 2
[1] "Progressive_BS_E0S2Y0TS"
[1] "Deceased_BS_0YWFFRYV" "Deceased_BS_3V7ZNBTG" "Deceased_BS_YTCYVVY9"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_0YWFFRYV-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_3V7ZNBTG-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_YTCYVVY9-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 3
[1] "Diagnosis_BS_NSWP72M6" "Progressive_BS_P3R9QZKP"
[3] "Recurrence_BS_Y386XSV3"
[1] "Deceased_BS_ERRA7V0W"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Diagnosis_BS_NSWP72M6-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Progressive_BS_P3R9QZKP-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Recurrence_BS_Y386XSV3-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 4
[1] "Diagnosis_BS_6GN1FGTB"
[1] "Deceased_BS_6VKKMM6M"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_RJ1TJ2KH-Diagnosis_BS_6GN1FGTB-vs-Deceased_BS_6VKKMM6M-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 3
[1] "PT_75HRTX4S" "PT_HFQNKP5X"
[1] 1
[1] "Diagnosis_BS_7YGM7F5R"
[1] "Deceased_BS_3CDQYJ5Q" "Deceased_BS_WTGPN218"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_3CDQYJ5Q-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_WTGPN218-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 2
[1] "Recurrence_BS_6F49F7WH" "Progressive_BS_9GN1QA3Q"
[3] "Progressive_BS_FBJ516WW"
[1] "Deceased_BS_2MPNPD28" "Deceased_BS_5B6XZ7YP" "Deceased_BS_FVPZ3CYY"
[4] "Deceased_BS_MAHWW7NR" "Deceased_BS_SCW1FS55" "Deceased_BS_VZB4K7NV"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 4
[1] "PT_19GCSK2S" "PT_5NS35B66" "PT_FA2F3HQG" "PT_GTHZF21E" "PT_KTRJ8TFY"
[6] "PT_KZ56XHJT" "PT_MNSEJCDM" "PT_PR4YBBH3"
[1] 1
[1] "Diagnosis_BS_3KD309X6"
[1] "Deceased_BS_AH252MTC" "Deceased_BS_FZ8D57HJ" "Deceased_BS_GH6PH611"
[4] "Deceased_BS_NXT37ZPA"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_AH252MTC-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_FZ8D57HJ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_GH6PH611-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_NXT37ZPA-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 2
[1] "Diagnosis_BS_SVKMG97S"
[1] "Deceased_BS_F0JN3TFM"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_5NS35B66-Diagnosis_BS_SVKMG97S-vs-Deceased_BS_F0JN3TFM-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 3
[1] "Diagnosis_BS_G9WRA2N1"
[1] "Deceased_BS_S78482NX"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_FA2F3HQG-Diagnosis_BS_G9WRA2N1-vs-Deceased_BS_S78482NX-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 4
[1] "Diagnosis_BS_N4S9T8F5"
[1] "Deceased_BS_3A7YMV93" "Deceased_BS_5PR4KXE1" "Deceased_BS_D3BH8D4Y"
[4] "Deceased_BS_EV071CE1" "Deceased_BS_FQBVBTCY" "Deceased_BS_M4KR9DSE"
[7] "Deceased_BS_T3WNX1E2" "Deceased_BS_Z7806Z75"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_3A7YMV93-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_5PR4KXE1-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_D3BH8D4Y-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_EV071CE1-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_FQBVBTCY-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_M4KR9DSE-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_T3WNX1E2-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_Z7806Z75-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 5
[1] "Diagnosis_BS_3VKW5988" "Diagnosis_BS_402W79TS" "Diagnosis_BS_BQ81D2BP"
[1] "Deceased_BS_5968GBGT" "Deceased_BS_AF5D41PD" "Deceased_BS_EE73VE7V"
[4] "Deceased_BS_HYKV2TH9"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 6
[1] "Progressive_BS_0ATJ22QA" "Progressive_BS_9DN4QR6E"
[3] "Diagnosis_BS_FWP8ZA4K" "Diagnosis_BS_H8NWA41N"
[1] "Deceased_BS_1Q524P3B" "Deceased_BS_22VCR7DF" "Deceased_BS_AK9BV52G"
[4] "Deceased_BS_D6STCMQS" "Deceased_BS_X5VN0FW0" "Deceased_BS_YHXMYDBN"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 7
[1] "Diagnosis_BS_CBMAWSAR" "Diagnosis_BS_ZSH09N84"
[1] "Deceased_BS_J8EH1N7V" "Deceased_BS_Y74XAFJX"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 8
[1] "Diagnosis_BS_PPY0EWPG"
[1] "Deceased_BS_C2NH5FDT"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_PR4YBBH3-Diagnosis_BS_PPY0EWPG-vs-Deceased_BS_C2NH5FDT-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 5
[1] "PT_DNAJYFZT" "PT_NJQ26FHN"
[1] 1
[1] "Recurrence_BS_EJ1H9PZY"
[1] "Deceased_BS_8XJJVBQP"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_DNAJYFZT-Recurrence_BS_EJ1H9PZY-vs-Deceased_BS_8XJJVBQP-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 2
[1] "Recurrence_BS_JZ61AA7Z" "Diagnosis_BS_NXTB7A9N"
[1] "Deceased_BS_7XEEQM3X" "Deceased_BS_AYR6PJN0"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 6
[1] "PT_HJMP6PH2"
[1] 1
[1] "Recurrence_BS_9SVMVJ45" "Diagnosis_BS_XKM2EAT4"
[1] "Deceased_BS_3XW15QAZ" "Deceased_BS_4CT3A9PQ" "Deceased_BS_FS48BMA3"
[4] "Deceased_BS_GXFX6VW1" "Deceased_BS_RNAADGMF"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_GXFX6VW1-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_GXFX6VW1-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_RNAADGMF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_RNAADGMF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 7
[1] "PT_37B5JRP1" "PT_394ZA6P7" "PT_3CHB9PK5" "PT_8GN3TQRM" "PT_KBFM551M"
[6] "PT_MDWPRDBT" "PT_Z4BF2NSB"
[1] 1
[1] "Diagnosis_BS_EJV0N3BX"
[1] "Deceased_BS_8Q8N6AHW"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_37B5JRP1-Diagnosis_BS_EJV0N3BX-vs-Deceased_BS_8Q8N6AHW-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 2
[1] "Diagnosis_BS_1KP6JADZ"
[1] "Deceased_BS_Q41J76W9"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_394ZA6P7-Diagnosis_BS_1KP6JADZ-vs-Deceased_BS_Q41J76W9-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 3
[1] "Diagnosis_BS_20TBZG09"
[1] "Deceased_BS_8AY2GM4G"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_3CHB9PK5-Diagnosis_BS_20TBZG09-vs-Deceased_BS_8AY2GM4G-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 4
[1] "Recurrence_BS_QQP17PDQ" "Progressive_BS_RXSBJ929"
[1] "Deceased_BS_S791VC80"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_8GN3TQRM-Recurrence_BS_QQP17PDQ-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_8GN3TQRM-Progressive_BS_RXSBJ929-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 5
[1] "Diagnosis_BS_9P4NDTKJ" "Diagnosis_BS_M0B42FPR" "Diagnosis_BS_M5FM63EB"
[4] "Diagnosis_BS_WYTDVC0Y"
[1] "Deceased_BS_J8EK6RNF"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_9P4NDTKJ-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_M0B42FPR-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_M5FM63EB-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_WYTDVC0Y-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 6
[1] "Recurrence_BS_00TRPEQX" "Recurrence_BS_BQWMQM2Y"
[3] "Progressive_BS_D368BNRD"
[1] "Deceased_BS_1M63B97V"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Recurrence_BS_00TRPEQX-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Recurrence_BS_BQWMQM2Y-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Progressive_BS_D368BNRD-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 7
[1] "Recurrence_BS_EJP43CD9" "Diagnosis_BS_W2QCHQ7E"
[1] "Deceased_BS_2T4EJ6KN" "Deceased_BS_537YFJ06" "Deceased_BS_C6T8F9K7"
[4] "Deceased_BS_GSXNQNRY" "Deceased_BS_M29BNE7Z" "Deceased_BS_MRN9VDQ0"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 8
[1] "PT_1H2REHT2"
[1] 1
[1] "Progressive_BS_79SYEHY3" "Progressive_BS_7M7JNG00"
[1] "Deceased_BS_96S0VQBN"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma,Low-grade glioma/PT_1H2REHT2-Progressive_BS_79SYEHY3-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma,Low-grade glioma/PT_1H2REHT2-Progressive_BS_7M7JNG00-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 9
[1] "PT_23NZGSRJ" "PT_CXT81GRM" "PT_NZ85YSJ1"
[1] 1
[1] "Diagnosis_BS_05S9WJW6"
[1] "Deceased_BS_209RV8H2" "Deceased_BS_CCHHH752" "Deceased_BS_CJ2G78ZZ"
[4] "Deceased_BS_F2MTFYFR" "Deceased_BS_GNXGGWFN" "Deceased_BS_H8JZ6CZR"
[7] "Deceased_BS_Q03MVGN6"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_209RV8H2-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CCHHH752-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CJ2G78ZZ-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_F2MTFYFR-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_GNXGGWFN-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_H8JZ6CZR-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_Q03MVGN6-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 2
[1] "Diagnosis_BS_HZNKSQ17"
[1] "Deceased_BS_3CG2N4PD"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_CXT81GRM-Diagnosis_BS_HZNKSQ17-vs-Deceased_BS_3CG2N4PD-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
[1] 3
[1] "Diagnosis_BS_4HRYS7JY"
[1] "Deceased_BS_Q7QH96SX"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_NZ85YSJ1-Diagnosis_BS_4HRYS7JY-vs-Deceased_BS_Q7QH96SX-vaf-corplot.pdf"
Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables
# Bind all df from list and save in one file
df_list_bind <- bind_rows(df_list) %>%
write_tsv(file.path(results_dir, "df_list_common_genes.tsv"))
sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggthemes_4.2.4 reshape2_1.4.4 ggrepel_0.9.3 lubridate_1.9.2
[5] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.1 purrr_1.0.1
[9] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.0
[13] tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 xfun_0.38 bslib_0.4.2 colorspace_2.1-0
[5] vctrs_0.6.2 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7
[9] utf8_1.2.3 rlang_1.1.0 jquerylib_0.1.4 pillar_1.9.0
[13] glue_1.6.2 withr_2.5.0 bit64_4.0.5 lifecycle_1.0.3
[17] plyr_1.8.8 munsell_0.5.0 gtable_0.3.3 evaluate_0.20
[21] labeling_0.4.2 knitr_1.42 tzdb_0.3.0 fastmap_1.1.1
[25] parallel_4.2.3 fansi_1.0.4 highr_0.10 Rcpp_1.0.10
[29] scales_1.2.1 cachem_1.0.7 vroom_1.6.1 jsonlite_1.8.4
[33] farver_2.1.1 bit_4.0.5 hms_1.1.3 digest_0.6.31
[37] stringi_1.7.12 rprojroot_2.0.3 cli_3.6.1 tools_4.2.3
[41] magrittr_2.0.3 sass_0.4.5 crayon_1.5.2 pkgconfig_2.0.3
[45] timechange_0.2.0 rmarkdown_2.21 R6_2.5.1 compiler_4.2.3